Stargate Atlantis: Philosopher's Stone
by the morrighan
Summary: The second half of my version of a season six. This is the third story.
1. Chapter 1

Stargate Atlantis: Philosopher's Stone

"John? John?"

John Sheppard blinked, rousing himself from his slumber. He rolled onto his back, opening his eyes. He was surprised to find himself on the floor when he could distinctly remember being slouched over the desk only a second ago. Maybe it had been two seconds as his brain felt foggy and slow to move from sleep to wakefulness.

He blearily stared up as fingers stroked down one side of his face. The touches were soft, gentle. "Huh? Moira?" he asked. The woman was out of focus, indistinct, but she reminded him of Moira even though she wasn't in Atlantis. He blinked again.

"John? John, you have to get moving. They shouldn't have left us, John. We were the last ones. John, please, don't let me die out here like this!"

"Whoa, what? Moira, Moira, wait! I'm coming!" He moved abruptly, getting to his feet. He froze. Moira, or rather the woman who had resembled her was gone. He was no longer in the bio lab.

There was chaos all around him in the control room. People were running, shouting. They were all strangers to John, men and women he had never seen before and they were all clad in harmonious garments of gray and green, the same tunic and pants he suddenly noticed he was wearing as well.

The city was tilting wildly as alarms shrieked like some insane banshee. Lights flickered and flashed in a green mosaic that was dizzying. It was listing crazily like a ship at sea about to be engulfed by a tidal wave and the chaos erupting wasn't helping the situation.

John realized he wasn't in Kansas anymore.

He grabbed onto a console as his feet threatened to slide out from under him. The console flared to life at his touch. A screen rose as the city canted again and he braced himself. An impact hit the Shield. The city had a pinkish glow for a moment, punctuated by staccato bursts of green and yellow as the impacts thudded, thudded but could not penetrate the Shield.

John eyed the screen. "Crap," he muttered. There were scores of enemy ships approaching and attacking. They were just blips on the screen but there were far too many of them and John wondered if they were Wraith or Replicators or something else. He suddenly realized the city wasn't on a planet. The city was flying. The city was a ship flying in outer space.

"About time, Seamus! Enemy craft bearing down on three sides!" snarled a man who was older and grizzled and a complete stranger to John. "There'll be no help from Atlantis this time! Damn Brendan and his damn explorations!"

"Atlantis? So this isn't Atlantis and we're not…Seamus?" John asked. His brows were quirking in puzzlement. Another hit sent the city spinning like a top.

"Sir! Falias is reporting heavy damage! They are unable to sustain the—"

"Jettison it!"

"Sir! There are still work crews in that area and we can't get to them to—" a woman with curly blond hair began to protest.

"Jettison it now!" the man ordered. "If we don't jettison it we risk losing the entire city! Do it!" he bellowed.

There was an odd hush, a moment of silence. There was a searing sound, just below the range of audible hearing. It was like a vibration that set one's teeth on edge. The city canted and John moved to the window with the rest to watch in shock and horror as one of the city's outer quadrants was violently disengaged from the rest.

Although space was silent it was too easy to imagine the screams of those still left there.

The section spun, spun, wobbling without being attached to the city. It was a lost section, a lamb bleating for its mother or for the shepherd to guide it back to the flock. John's hands touched the cold, cold wall as the portion of the city spun and spun, getting further and further away until it was suddenly obliterated by a flash of green laser fire.

The explosion was bright, so bright the city compensated and darkened the viewports until the danger was past.

But the danger was only just beginning.

"We never should have come to this galaxy!" a man moaned.

People were moving, shifting around him, returning to their work stations. "Wait, we're not in the Pegasus…then where the hell are we?" John asked, turning towards the main controls. "And who is firing upon us?"

"Seamus! Why aren't you in the Chair? Coordinate with Fachtna and get us home now! As soon as we reach home we are going to ground! The Stargate's inoperable out here but we can seal the hyperspace window so they can't follow us! Go!"

"Going!" John replied, taking off at a sprint. There wasn't time to explain he wasn't this Seamus guy and didn't even belong here, wherever here was. The pieces were falling together and he was beginning to figure out where he was but not when. He rushed to the lower levels, trusting that the blueprint of this city would match Atlantis, or nearly so.

"About time, Seamus! Come on! It will take two of us to get her home in one piece!" A red-haired man harangued from one of two Ancient Chairs, working in tandem.

John blinked at the Irish accent, but quickly slid into the vacant Ancient Chair. Instantly it reclined as the power engulfed him, grabbing him. He closed his eyes. "Whoa!" The rush was intense, virile. Suddenly he was the city, feeling every hit, feeling every bombardment as the city flew a wild course in space. He commanded Drones and flew them in concert with the other man, directing them towards a fleet of massive ships that John tried to identify.

When he saw the markings on the ships he knew.

"Fuglies! We're fighting fuglies…we must be in their galaxy, but when?" he muttered. He opened his eyes, needing answers, breaking concentration but he was physically pulled back against the chair by an unseen force. His palms were stuck to the arm pads and he grunted with the effort of trying to release them. Suddenly the city was in control instead of the other way round and he didn't like that, not at all.

"Seamus, concentrate! We need to buy time to get away!" Fachtna ordered.

John swore but closed his eyes again, trying to relax into the power. It was much stronger here, and he wondered if that was the result of this city having fully loaded ZPMs. Or perhaps this city's sentience was stronger than the one on Atlantis. He didn't have time to ponder as he directed another wave of Drones towards the enemy ships.

Explosions ripped and rippled but did minimal damage as the ships kept coming.

"Forget the Drones!" sounded the ornery voice of the commander. "Initiate evasive actions! We'll open the hyperspace window and lock the ninth chevron!"

"Understood, sir!" Fachtna replied. "Seamus, with me! We never should have come here! Damn Finegas and his experiments!"

"Wait, wait, when is this? You encountered the fuglies in their own galaxy but left scant records of it! Did you create them? I need all the intel you have on them now! I need to know how to defeat them and how to OW!" Pain flared. It was as if a giant hand was slamming him back into the Chair, effectively pinning him there as a prisoner. "Let me go! Damn it, I'm not this Seamus guy! I am John Sheppard from Atlantis, from the future! I need to find this city to save her! I need to get outta here!"

John closed his eyes, concentrating not on the firefight around him but on Atlantis, on returning there. But when he opened his eyes he was still locked in the Chair. He knew he wasn't in some stasis pod trapped in some virtual reality like he had been on the Aurora but it was worth a shot.

Except that it hadn't worked.

"Concentrate, Seamus and stop babbling! It will take two of us to get us home!"

"I'm not babbling, damn it! I don't belong here!" He cursed, struggling. It was like he was glued to the Chair, being forced against his will to help these people and this city in a past confrontation that was already lost, or had been lost. He really didn't know.

And he really didn't care.

He just wanted to go home.


	2. Chapter 2

Stargate Atlantis: Philosopher's Stone2

Alan Simmons was angry as he stomped towards the bio lab. He was clutching a data pad under his arm. Years of research were contained within it, and more importantly his latest analysis of the new alien species was compiled into a very thorough and precise report. The same report that Colonel Sheppard had rejected without even reading it which was an insult. For some reason the military commander preferred the wild theorizing of one of Alan's subordinates, and Alan was not going to allow that to stand.

He planned to issue a formal complaint to Mr. Woolsey as soon as he could.

He entered the lab, striding to his desk but he paused. The lab was oddly dark. The lights were flickering, flickering. He moved to the panel, touching it and trying to adjust the illumination. Nothing happened. He looked round. The room was cold, very cold, although no air was blowing from the vents. He stared at the floor. There was a boot protruding from behind a work station. He set down his data pad and neared cautiously.

The boot was connected to a leg, the leg to a body sprawled on the floor near an upturned chair. The blackness of the man's clothes almost concealed him in the blackness of the room, but as the lights abruptly flared to life his identity was revealed.

John Sheppard.

Alan stared a moment. The colonel appeared to be unharmed, but unconscious. Alan could see no obvious sign of injury, and the colonel was still breathing, albeit slowly. There was a tiny pool of blood near his face from a nosebleed. Alan felt a sense of satisfaction, seeing the very man who had ridiculed him and ignored him on the floor like this. Common sense and decency took over, however, and he knelt to check John's pulse. At the same time he tapped his earpiece to request medical assistance.

As much he disliked the man Alan did not want John's death on his hands.

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"Gently now, easy does it!" Carson Beckett guided the medical team as they carefully placed the military commander onto a bed in the infirmary. They backed away as Carson neared. He checked John's pulse, checked his heartbeat. He shone a light into each green eye, pulling up the lid to check for dilation and any kind of reaction. "John? John, can you hear me? John?" He nodded and a nurse gently swabbed at John's bloody nose and chin.

"What happened to him?" Richard Woolsey asked, staring at the prone body of the military commander.

"I don't know…" Carson frowned, checking John's head for any signs of injury. He drew a scanner to him and ran the machine over John's body. The green beam ran from head to toes and back again. "No injury, nothing internal, no bleeding except for that bloody nose and that's almost gone. He's fine."

"Fine? He's unconscious and unresponsive! How is that fine?" Rodney McKay flared angrily. He stared at his friend, wringing his hands together.

"Physically he's fine," Carson clarified. "It's like he's in a deep sleep, a very deep sleep, but not a coma. His neurons are firing at an exponential rate so there is nothing wrong with his brain, and his vital organs are functioning properly, just at a slower rate."

"What does that mean? Why won't he wake up?" Ann Teldy asked. She stood near the bed, starring down at the man she loved. Dread clouded her heart.

"I don't know. You found him in the bio lab?" Carson asked.

All eyes swung to Alan. The biologist shrugged. "Yes. In the back on the floor. The lights weren't working either," he added, as if that explained everything.

"What the heck was he doing in the bio lab?" Rodney wondered.

Carson was nodding. He moved to John and checked his pulse again. "Steady, but slow. I suspect he was connecting deeply to the city again."

"What? You mean the, the city did this?" Richard asked, baffled.

"In a manner of speaking yes. I can't be sure, of course…but it's the only thing that makes sense. I've been doing some research on the ATA gene and its interaction with the city and the systems that it can activate and control to a certain extent."

"Wait, wait, the city did this? Really? Because he was looking for something?" Rodney asked. He couldn't wrap his mind around it and he was shaking his head.

"Yes, Rodney. I'm going to run some brain scans, and check his brain wave patterns. We need to determine where he is."

"What? He's right there!" Rodney exclaimed, but he froze, eyes widening. "You mean he's in some virtual reality or even the computer system? Then hook me up and I can pull him out like he did for me that last time, remember? Oh right, you weren't…anyway, we were in each other's brains and dreams to get rid of that alien intelligence and I can do it again!" He was already moving to the next bed.

"That won't work, Rodney. It's not like that. This is much more sophisticated. It's not an alien intelligence but the city. I don't think it will harm him, but if he doesn't regain consciousness soon I may have to force him out of it."

"And by force you mean…"

"I mean shock his system to awaken his brain from the hold that is on it."

"What can I do?" Ann had regained her composure and stood solemnly, her blue eyes full of concern and gravity.

Carson kindly smiled at her. "Sit with him. Talk to him. On some level I believe that he can hear you. Talk to him and keep him grounded here. We have to trust he will break free of it, or the city will release him once it has shown him whatever he needs to see."

"Keep me apprised. Do whatever you can, Doctor Beckett." Richard sighed, and after a last look he left the infirmary. Atlantis was a wondrous place, but it could also be terrifying.

Rodney grabbed a chair and sat near the bed. "I'm not leaving. I still think if we linked up our brains I could enter wherever he is and get him out of there."

"This is not the same, Rodney," Carson tiredly repeated. He moved to a cabinet full of drugs and other medical necessities.

Rodney followed, jumping to his feet. "So that's it? You're just going to do nothing!"

Carson whirled, suddenly angry. "I'm doing all that I bloody can but the truth is the city's AI is in control and until it lets him go or John breaks the link there's not a bloody thing I can do except keep him stabilized and alive!"

Rodney blinked. "Okay then."

Carson looked to see everyone staring at him. Any outburst from the doctor was extremely unusual. Then again he wasn't the original Carson Beckett but a clone whose slightly differing experiences may have altered his blueprint personality. He saw Alison's startled gaze and he turned back to the cabinet. "I'll do what I can, and I will pull him out by force if necessary. See if you can find out whatever he was researching. It might give me a clue."

"You, um, you don't think the same thing will happen to me, do you?" Rodney asked.

Carson smiled as he faced the worried physicist. "No. You don't need to access any restricted files. Just see what's on that monitor in the bio lab, if anything is there."

"Okay. I'd hack those files, though, if it would mean helping John." Rodney glanced at the prone, unconscious figure of his friend. Ann was sitting close, her hand on his arm as she stared worriedly at him.

"I know that you would, Rodney. If you find anything let me know."

As Rodney left Alison approached. "Do you really think the answer is there?" she softly asked.

Carson shrugged. "I don't know. Maybe. At least it gives him something to do besides pestering me. Keep an eye on his vitals. I am going to see if I can find anything in our notes."

Alison caught his arm as he tried to move away from her. "You're not going to do what he did, are you?"

"No. Not unless I have to, that is," he said somberly, but he added with a shrug, "first I have to discover exactly what he did."


	3. Chapter 3

Stargate Atlantis: Philosopher's Stone3

The ship shook violently and John forgot about his protests, his fighting and his attitude. This was a battle for survival and even if this wasn't real he didn't want to be on the losing end. His hands clung to the arm pads and he shut his eyes, concentrating. Explosions rippled around him as he saw the glimmer of the hyperspace window yawning in the distance, a sudden blur of bright light amid the sea of darkness.

"Sir! Murias is reporting heavy damage and a sixty-percent Shield loss!"

"Keep her intact! We're heading for the window! On my mark plow the field with the Drones and then we'll fly an erratic Gamma pattern to throw them off the scent!" John took command as he directed the ship, the Drones, even his companion in the Chair next to him. The restraints eased as he took charge, as if now that he was obeying the city it felt he could be trusted to stay and do his job.

John could breathe easier and he slightly relaxed as he was no longer trapped and held against his will. Sweat was beading along his scalp and his neck. His muscles were straining. Abruptly the city whirled and he had the sickening sensation of vertigo, as if was flying upside down and the Chair was attached to the ceiling and not to the floor. He adjusted automatically, his years of flying fighter jets taking over as his mind compensated and his body adjusted to the sudden loss of gravity.

His companion was not so lucky and he groaned, almost retching but he clung to the Chair and followed after John's lead. "What the hell is Gamma?" he managed to croak.

"Just trust me! Here we go! Loop the loop!" John had never attempted this maneuver with a large plane, not to mention a huge spaceship but he knew it was their only chance. The lasers of the enemy were becoming more accurate as the flight pattern was too predictable.

"Seamus, hold this vector! The window is viable in thirty seconds!"

"Can we hold them off for that long?" Fachtna asked.

"We don't have a choice! And stop calling me Seamus!" John snarled. He dove towards the flare of light in space, jinking and juking the city ship to avoid enemy fire. The Drones were gone, hammering the ships behind them. They were gaining speed, looping and whirling like a spinning top. "Just like Beggar's Canyon and back home."

"What?"

"Never mind," John sighed.

"Shields at seventy percent and dropping!"

"She'll hold! She'll hold! Hold together, baby, we're almost there!" John grunted. They flipped again and John felt he was once more on the floor instead of the ceiling. He remembered to compensate since the city had lost one of its sections and was currently wobbling like a broken toy. He tried to pull it all together, to seam over the gaping wound with the Shield as best he could.

"Findias tower is clipped! The Shield is penetrated and we—" the warning was drowned by a wailing alarm.

John ignored it all. He swerved and directed the ship directly into the light. It blinded him, even with his eyes closed and he felt his whole body tense and spasm before he collapsed backwards into the Chair. In the distance he heard another explosion, felt the vibration as a ZPM stuttered and came close to shattering.

A high-pitched whining filled his ears and set his teeth on edge.

All went black.

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"John? John, wake up."

John tried to open his eyes. They were heavy as rocks and it took sheer willpower for him to open each eyelid. His vision was a blur of lights until he squinted. He felt exhausted, sore, weighed down by a ton of rocks although there was nothing on him but a blanket. He was reclining on a bed. "Moira?" he asked. The hazy figure of a woman was near him, indistinct except for the fall of brown hair and gleaming brown eyes. His voice was raw and it hurt to speak. He licked his lips but even that simple act caused fatigue.

Fingers touched his face. They were cool caresses on his hot, sweaty skin. "John, you have to get up. They're coming, John. They found a way in and they are coming for what we took. They won't stop until they reach you. It's too late for me." There was a depthless sorrow in her eyes, in her voice that tore at John.

"No, no…I can stop them and save you…" he muttered, trying to move. He blinked several times but her image was still an indistinct blur. He couldn't see her clearly so his mind filled in the details, details that he wanted to see, that he needed to see. He tried to reach out to her, to touch her wrist but his arm was heavy as lead.

He could barely move his fingers as the lethargy consumed him.

"No, no, my lad, settle." A man stepped to John, seeming to step through the woman as she melted into nothing. The man pushed John back onto the bed. "Easy, Seamus. You took quite a beating but you got us home and you made it. I'm afraid Fachtna wasn't so lucky."

"Huh?" John was thrown by the Irish accent, as well as the loss of the woman. Even her touch had dissipated. He stared round but she was gone. He looked over to see a covered body on the bed next to his. There were splatters of blood on the crisp white sheet.

"It was too much for him," the doctor explained. "The interface. We always knew it was a risk with twice the power and twice the Chair potential but we had no choice. We're here now. We're going to ground so they can't detect us in case they get through. Using the ninth chevron we've locked the way but we are taking precautions, just in case. We've sent word to Atlantis but so far they have been unresponsive."

"Fighting the Wraith…they, they left. They left and sank the city…" John tried to remember but his mind was clouded and murky. The past and the future were merging and he couldn't tell which was which anymore.

"What? Don't be daft, man! They are winning that war. To be sure they will be wroth with us for trespassing against the laws but when they see what we've discovered and stored in Gorias they will forgive us all. We will gate to Atlantis."

"No, you…what did you find? What did you take from the fuglies? Will it defeat them? You can't gate to Atlantis, it's gone! I mean it's under the ocean now, then, back then or now…oh crap I hate this stuff," he moaned. "What did you—"

"We made it, Seamus, that's all that matters. Get some rest and stop talking to your aisling."

"My what? Wait, wait!" John swore and struggled to his feet as the doctor strode away from him. "Wait! You can't reach Atlantis! The 'Gate is inactive now, I think. Wait! They are losing the war with the Wraith! They lost! I'm from the future and I need all the intel you have on the fuglies because they are coming now, to my Atlantis! Listen to me! Where the hell is Moira? Moira can explain all this Irish gibberish and I need a beer!" He touched his nose. Scarlet drops stained his hand. Men were heading for him and forced him back to the bed as they grabbed him. "Let go of me!"

"Easy, Seamus. Disorientation is only natural," the doctor soothed as he returned. He held a narrow piece of equipment and pointed it towards John. "Just relax and you'll feel like your old self soon enough. Is your aisling talking again?"

"My what? Listen to me! My name is John Sheppard and I am from Earth, currently stationed at Atlantis! We found the city after thousands of years when it lost the war to the Wraith and I need your help now to fight the fuglies because they are coming and."

The shot made John fall back onto the bed as he was rendered unconscious again.

The doctor sighed. "He's in a very bad way, just like the last time. Take him to his room and keep him locked down until we dial Atlantis. I only hope he survives."


	4. Chapter 4

Stargate Atlantis: Philosopher's Stone4

Carson squeezed the bridge of his nose, closing his eyes for a moment. He sat hunched over his desk while data scrolled and scrolled on the monitor in front of him. He had been at it for hours now and the words were blurring into gibberish. He sat up, blinking and looked away from the brightness of the screen. Ronon Dex was standing near, towering over the doctor with a stern expression on his face. "There's been no change."

Ronon frowned. "Is there anything we can do?"

"No. I've been researching all I can about the ATA and the city and frankly it's beyond me. The good news is that so far he's been stable."

"Then why doesn't he wake up?" Ronon glanced over to see Ann and Teyla Emmagan sitting on either side of the military commander. Both appeared worried.

"I don't know." Carson sighed. He looked past Ronon to see Rodney approaching, data pad under one arm. "Anything?"

"Nothing." The physicist was clearly annoyed and frustrated as he set the data pad onto the desk. "Whatever he was doing on that computer it's gone now. There's not a trace, not even a history as to where he went. And his data pad is encrypted. Believe me, I tried everything I could think of but it won't let me in. I have no idea what his password could be. And when I tried to check the hard drives of that other system it blocked me at every turn and I got a headache so I had to stop for now." He sighed. "Only he can tell us what he was doing. Has there been any change?"

"No, but he's stable." Carson moved to his feet, glancing over at another desk where Alison was working with the same lack of success. "Take a look at this." He walked over to a host of machines that were monitoring John's vital signs. "This is his brain activity. As you can see the excited neurons are firing at a rapidly advancing rate. But then there's this." He pointed to a jumping line that was below the first one, nearly mimicking the other one.

"Is that another brain wave?" Rodney asked.

"No. That is the city."

"What?" Rodney exclaimed, staring.

"The city has a brain wave?" Ronon asked, equally surprised.

"No. Yes. Well, sort of. I am detecting two patterns in his head, one is his and the other must be the city's. As you know when we connect to the city via the ATA there is a strong mental component to it, as our brains link to the city's limited AI."

"Are you saying he has two separate thought patterns in his head, like I did?"

"No, because this one isn't a human consciousness but a machine's and therefore it is not a consciousness, so to speak but something else. I can't quite explain it, Rodney. I've never been that connected to the interface."

"Are you saying this city has a, a brain? It has a consciousness?" Ronon inquired.

"In a manner of speaking, yes. It's artificial but was programmed by humans, by the Ancients so it will exhibit human characteristics. It's not a living organism like a Wraith ship, for instance, but it is a very sophisticated interactive technology with limited thought patterns that were programmed into it."

"And if I try to reprogram it?" Rodney asked.

"It could cause John irreparable harm while it is in his head."

"So we need to get it out of his head. How?" Ronon asked.

"That's the six million dollar question, son. I think John is strong enough to sever the link if he wanted to do that. Trouble is he may not want to until he gets what he wants."

"Wait…so all we need to do is to tell the city to let him go!" Rodney snapped his fingers. "If you get into the Chair and connect to the interface you could do that!"

"I thought of that, but I don't think it will work."

"Why not?" Ronon asked. He found all this talk of the city as if it was a living thing somewhat unnerving, but he trusted the judgment of his friends.

"There are several levels of consciousness. Think of it as a building with several stories. We could be on one floor while John is several floors above us, and the city would block us."

"Then we explore floor by floor and I can bypass the city's firewalls and—"

"It's not a computer, Rodney! I mean it is, but it's much more sophisticated than that! In essence it is a living being, but with far more intrinsic control than we would have."

"So any interference would cause more harm than good," Rodney realized. "Damn it! There has to be something we can do!"

"There is. We are doing it." Carson looked over at the bed. Ann and Teyla were quietly talking, their voices soft whispers crossing back and forth over John's inert form. So far he had been completely unresponsive. Something was nagging at the doctor but he couldn't quite place it, not yet. He stared at his patient. "He was found in the bio lab, right?"

"Yes. Is there some significance to that?" Rodney asked.

"There could be." Carson walked over to the bed, ignoring the puzzled glances of Rodney and Ronon. He smiled. "Excuse me, ladies. Could you step over there for a wee moment?"

"Of course, Carson." Teyla said. She led Ann to where Ronon and Rodney stood.

Carson checked John's vitals. He adjusted the twin pads on either side of his temples as they recorded his brain activity. "Now, son, I think I know why you were in the bio lab. The question is do you?" he said quietly, leaning over his patient.

"Has there been any change?" Richard asked, joining them.

"No, not yet," Rodney answered. All were watching as the doctor was leaning over John, adjusting equipment and talking in low tones.

"What's he doing?" Richard asked.

"I have no idea," Rodney answered.

"We have been talking to him for an hour and John has not moved at all," Teyla said.

"There must be some way to awaken him," Ann insisted.

"If we cut the power to the city would it—" Richard suggested.

"Kill him. It would kill him," Ronon replied.

"What if we moved him out of the city?" Rodney suggested. "If he was away from the city perhaps the hold wouldn't be as strong."

"That is a very good idea, Rodney," Richard replied.

"Can he be moved safely?" Teyla asked.

"We should take him in a Jumper to the mainland. That should be far enough," Ann suggested.

Everyone was becoming excited by the idea and the hope that it offered. They eyed each other, exchanging smiles of encouragement.

"Carson! We've got a plan to move John out of the city!" Rodney announced, heading for the doctor.

Carson held up his hand, stopping the physicist in his tracks. "There's no need. I have an idea." He turned to his friends as they all watched him, hope on their faces. "I'll need a headset."

"For yourself?"

"No, Teyla. For John. I have an idea."


	5. Chapter 5

Stargate Atlantis: Philosopher's Stone5

"John? John?"

John opened his eyes. He was on a bed in a room that resembled his but clearly wasn't his. There were marked differences. There was no fridge. There was no Johnny Cash poster on the wall. There was an odd painting of greens and blues depicting a hilly landscape sloping down to a turgid ocean. He blinked to see a woman sitting close to him, stroking his hair. Her fingers were cold, soothing and gentle. John smiled. "Moira? How are you here? Wait…you're not Moira, are you?"

"John, you must go now. If you don't leave now you will never leave. You will never find me and you will leave her bereft."

"Find you? You're right here," he argued. "I…oh." He stared as he reached to touch her and his hand passed through her. "You're not Moira, are you?"

"No. Go now, John. Go before it is too late. Before you lose everything."

"Everything? I don't understand. I…Moira, no! Wait, wait, damn it!" He grabbed for her but she dissolved into the air. He sat, swinging his legs over the side of the bed. "How do I get out of her, exactly?" He looked down at his shoes. They weren't red ruby slippers but he clicked his heels together three times anyway. "There's no place like home. There's no place like home. There's no place like Atlantis," he muttered as he closed his eyes.

He opened his eyes to find himself in the same room. Men had entered and were staring at him as if he had lost his mind. He shrugged. "It was worth a try. Atlantis! I've seen enough now, baby, so let me go, all right?"

"Seamus, Seamus, still talking to your aisling? You need to get a grip, man!" The doctor neared, holding a large syringe with a long, long needle.

"Um, yeah, I guess I banged my head back there pretty hard. I'm fine now, really," John assured, backing up as his gaze was locked on that syringe and the men who were slowly surrounding him. "Look, I'm fine after my little nap here. We're back home, right?"

"Yes, and we are going to gate to Atlantis. But someone has to stay behind to secure the city and keep her hidden."

"Ah. And I'm guessing that would be me. All right, fine, I'll do it."

"No, Seamus, not you. We need you to connect to the interface again and get the Stargate functioning. I'm afraid that the strain may prove to be fatal, however, so I am going to give you a stimulant to keep you alive long enough for us to make it through."

John held up his hands, slowly backing away from the men towards the doorway. He knew the room behind him was a dead-end but he thought if he could make it there he could barricade himself in and find a way to get out of this dream or nightmare or virtual reality or whatever the hell it was. He didn't have time to analyze it. "That sounds great. Just great. Give me a minute to prepare, would ya?"

"I'm afraid not, Seamus. Take him."

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"Here we go now." Carson slid the headset over John's ears. He switched on the digital recorder and stepped back, glancing at the monitors.

"What is he listening to?" Rodney asked.

"A science report."

"You're going to bore him awake?" Ronon asked.

"Only if it had been one of Rodney's," Carson said with a smile. The physicist glared at him.

"I do not understand. How could a report awaken him?" Teyla asked.

"We've been talking to him for hours now. How could a recorded voice do what live voices couldn't?" asked Ann.

Carson ignored the questions, finding it a bit awkward to answer. Instead he increased the volume of the headset and waited.

XxX XxX XxX XxX XxX XxX XxX XxX XxX XxX XxX XxX XxX XxX XxX XxX XxX

The first blow rapped into a man's jaw. A kick sent the second one sprawling. John pivoted, and dove into the other room. He shut the door and locked it, whirling to look for an exit although he knew there wasn't one. The men were pounding on the door.

"Seamus! Seamus, don't be an arse! We can override this!"

"Crap." John looked round for a weapon, any weapon but the room was barren. He watched as sparks flew. The door was being forced open. "I could use a little help here, Moira or whatever your name is! Hey, Atlantis, this is enough, okay? Get me back now! If I'm stuck here I won't be of any use to you! I…hey, hey!" He moved to the window. He braced himself and struck it with his elbow. Glass shattered and flew to the ocean several feet below him. John leaned out. The wind struck him. He had heard a faint voice, familiar to his ears. "Hey! Hey, is that you?"

"Seamus! Grab the fool, would you?"

The men advanced to snatch John out of the window.

John flung himself out of the window with a smile.

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"…at least two hundred chemicals long as opposed to RNA which is only four letters long. It plays multiple roles in the DNA chains to keep proper cellular development ticking along but it also gives evolution a sort of blueprint, a molecular mold form which it can use to create new designs. As new proteins rarely appear there is a limited set of tools and materials from which to form new lincRNA but they develop all of the time. Humans have several of these, as you know, and they are found in no other species. I have found them in the new species thus proving that they are in fact, human, or rather a species of human and as Colonel Sheppard has insisted on all research being diverted directly to him I have transcribed the entire…"

"Ugh..Moira, enough of the science, please," John muttered, stirring on the bed. He groaned, blinking against the harsh light and trying to get away from the voice penetrating his head.

"John! Easy now, John!" Carson grinned and removed the headset.

"John, John, thank God!" Ann rushed to his side and touched his arm. Everyone crowded round the bed.

John blinked, hearing the woman's voice, but he stared as it didn't match the woman who had been talking in his head. He stared at Ann, realizing he was back home. He was in Atlantis.

"John! About time!" Rodney scolded, but relief was a cold wash over him.

"You gave us quite a scare, colonel," Teyla chided with a smile.

"Where were you?" Ronon asked.

John met their gazes, mind clearing. "I'm back."

"Yes, John, you are," Carson assured. He glanced at the monitor. Only one brain wave pattern was being recorded now.

"Where did you go? I mean you were here the entire time, but where were you?" Rodney inquired. "What the hell were you researching? Why were you in the bio lab? How did the city do that to you? Was it the city? Is it truly sentient like that? Did you—"

"Enough, Rodney! Let the man rest, would you?"

"Rest? He's been unconscious for hours, Carson!"

"Hours? It felt like days," John muttered. He rubbed his temple. He found himself reluctant to talk about it, although he remembered everything. "I'm fine, really. I guess I got in too deep. It won't happen again."

"Glad to have you back, colonel. Get some rest," Richard said. He let himself sag with relief. The thought of losing John at this critical juncture was untenable.

"Everything's fine, John. Nothing has changed," Ann assured with a smile. She moved close and brushed her lips across his.

John nodded as his friends moved away and out of the infirmary. He looked at the headset. He lifted it to hear the woman's voice still talking in there, going on about DNA and RNA. He frowned, handing the headset to Carson. "That woke me?"

"Yes." Carson smiled, shutting off the recorder.

"I'm surprised it didn't bore me to death," he jested. Carson was still smiling and John felt distinctly uncomfortable suddenly.

"Get some rest, John. Like Ann said, everything's fine and nothing has changed."

John nodded, settling back onto the bed. He folded his hands across his waist, staring at nothing as his thoughts flitted to several things at once. The things he had seen, the things he had been shown. Names and words he needed to have translated and explained for him. At least Atlantis was safe and secure, for now. Everything did appear to be fine.

Carson was wrong on one point, however.

Everything had changed.


End file.
